About the Project
Find hidden microproteins made by host and bacteria during infection, with proteomics and Ribo-seq, at the ICR, London. Not open if you spent over 12 months in the UK in the 3 years before the start.
Why it matters
Many small open reading frames (smORFs) are translated into microproteins that reference catalogs have long overlooked. During infection, both host and pathogen switch on new translation programs, and some of these microproteins likely act at the host-pathogen interface. Detecting them when host and bacterial proteins are mixed together is technically hard and largely unexplored.
The project
You will map microproteins during infection with Citrobacter rodentium, a model for gut infection, combining a dual bacterial-host proteomics workflow with Ribo-seq to capture translation on both sides across the stages of infection.
What you will do
- Map the microprotein landscape from early to peak to resolution of infection, in mouse epithelial cell lines and in vivo
- Use proximity labeling (BioID) to find interaction partners of infection-induced microproteins
- Validate interactions with thermal proteome profiling and targeted mass spectrometry
- Deliver a dual-species microprotein discovery workflow other groups can adopt
About ORFeus
This PhD is one of 15 in ORFeus, a Marie Skłodowska-Curie Actions Doctoral Network funded by Horizon Europe. ORFeus brings together 15 research groups in eight European countries, with industry and research partners, to study the dark proteome: the many microproteins made from small open reading frames long dismissed as non-coding. Together, the 15 projects aim to find these proteins, understand what they do, and test their potential in diagnosis, immunotherapy and drug development, with a strong focus on cancer.
Where you will work
You will join the group of Prof. Jyoti Choudhary at The Institute of Cancer Research (ICR) in London, which develops functional proteomics and mass-spectrometry methods and applies them to host-pathogen interactions. You will work closely with the group of Prof. Petra Van Damme at Ghent University, which brings microprotein proteomics expertise, including dual-proteome work on Salmonella infection.
Who should apply
We welcome applications from proteomics, biochemistry, mass spectrometry and microbiology graduates with an interest in infection biology.
- A master's degree (or equivalent) in biochemistry, proteomics, molecular or cell biology, microbiology, bioinformatics, or a related field
- Hands-on experience with mass-spectrometry proteomics or a related experimental technique, and comfort with omics data analysis
- Good written and spoken English
- Nice to have: Ribo-seq or NGS, BioID, infection biology, bacterial systems or mouse models
Eligibility (MSCA mobility rule)
You are not eligible if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (around March 2027). This applies whatever your nationality, UK citizens included. For example, a one-year UK master's plus a few more months in the UK already goes over the limit. Compulsory national service, short stays such as holidays, and time spent in a refugee status procedure do not count. Studied or worked in the UK recently? You are likely eligible for our 11 ORFeus positions outside the UK.
You must not hold a doctoral degree. Any nationality may apply.
What we offer
- A 36-month, full-time employment contract with full social security, under MSCA rules
- Supervision by Prof. Jyoti Choudhary and Prof. Petra Van Damme, with mentoring from partners across academia and industry
- A secondment of around three months at Tesorai (US)
- Training with 14 other ORFeus PhD candidates across Europe: network schools, workshops, transferable skills and international conferences
- PhD enrollment at the University of London, through the ICR
Practical details
Start around March 2027; the exact date depends on the host institution. Reference letters are requested only at the interview stage.
How to apply
You can only apply via https://www.orfeus-dn.eu/apply/. You can apply to up to three of the 15 ORFeus projects and rank them; every project you rank considers you. The application asks for:
- a few eligibility questions
- a short motivation per project (150 to 200 words)
- your experience with the project's key techniques
- your CV
- an overview of your bachelor's and master's grades, in one PDF
- contact details for two referees
- a short motivational video
Funding Notes
Fully funded 36-month employment contract in ORFeus, an MSCA Doctoral Network (Horizon Europe, GA 101309891), with full social security. A salary, not a stipend. Salary details for this position are on the application page. Open to all nationalities. UK mobility rule: you are not eligible if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (around March 2027), whatever your nationality. Applicants must not hold a doctoral degree. ORFeus positions outside the UK are open to UK residents: orfeus-dn.eu/apply.
